Formaline emits warnings while creating/updating the configuration git repository when a thorn contains symbolic links, for example in GRHayL/GRHayLib/src:

Formaline: Creating configuration git repository...
Formaline: Updating files in git repository...
WARNING: Refusing to add "arrangements/GRHayL/GRHayLib/src/Neutrinos" as it is not a regular file at Cactus/configs/etbhahaha/scratch/Formaline/bin/update-git-repo.pl line 202, <STDIN> line 6246.
...
fatal: bad revision 'HEAD'
Formaline: Committing source tree to git repository...

The full set of warnings occurs for the symlinked GRHayLib/src entries such as Neutrinos, Induction, Flux_Source, Reconstruction, Atmosphere, EOS, include, GRHayL_Core, and Con2Prim.

Root Cause

Formaline/src/util/update-git-repo.pl currently accepts only regular files before adding paths to the Formaline git repository:

if (! -e $file) {
  push @to_remove, $file;
  next;
} elsif (! -f $file) {
  warn "WARNING: Refusing to add \"$file\" as it is not a regular file";
  next--

Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2943/formaline-rejects-valid-symlinks-in